The problem here is that you are trying to use a Javascript type in a C# script. Because the two are compiled separately, you can’t use types from one with the other.
Basically this is a good case for picking one language (be it C#, JS or Boo) and sticking with it for everything- the languages aren’t fantastic at communicating with each other.
You can create a folder Assets/Scripts (or the name you prefer), and put your JS scripts there. Unity compiles Assets/Plugins, Assets/Standard Assets and Assets/Pro Standard Assets first, then the Editor subfolders inside them, and finally the scrips stored in other folders - like the Assets/Scripts I suggested. Scripts compiled in the first wave can be “seen” by scripts compiled after, thus the JS scripts will be able to use CS scripts in Plugins - but not the other way around: a script already compiled can’t see the others compiled after.